Constructor and Description |
---|
GSDI(Phylogeny gene_tree,
Phylogeny species_tree,
boolean most_parsimonious_duplication_model,
boolean strip_gene_tree,
boolean strip_species_tree) |
GSDI(Phylogeny gene_tree,
Phylogeny species_tree,
boolean most_parsimonious_duplication_model,
boolean strip_gene_tree,
boolean strip_species_tree,
boolean transfer_taxonomy) |
Modifier and Type | Method and Description |
---|---|
int |
getDuplicationsSum() |
java.util.Set<PhylogenyNode> |
getMappedExternalSpeciesTreeNodes() |
java.util.SortedSet<java.lang.String> |
getReMappedScientificNamesFromGeneTree() |
int |
getSpeciationOrDuplicationEventsSum() |
int |
getSpeciationsSum() |
java.util.List<PhylogenyNode> |
getStrippedExternalGeneTreeNodes() |
java.util.List<PhylogenyNode> |
getStrippedSpeciesTreeNodes() |
SDIutil.TaxonomyComparisonBase |
getTaxCompBase() |
java.lang.String |
toString() |
public GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree) throws SDIException
SDIException
public GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy) throws SDIException
SDIException
public int getDuplicationsSum()
public java.util.Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()
getMappedExternalSpeciesTreeNodes
in interface GSDII
public final java.util.SortedSet<java.lang.String> getReMappedScientificNamesFromGeneTree()
getReMappedScientificNamesFromGeneTree
in interface GSDII
public final int getSpeciationOrDuplicationEventsSum()
public final int getSpeciationsSum()
getSpeciationsSum
in interface GSDII
public java.util.List<PhylogenyNode> getStrippedExternalGeneTreeNodes()
getStrippedExternalGeneTreeNodes
in interface GSDII
public java.util.List<PhylogenyNode> getStrippedSpeciesTreeNodes()
getStrippedSpeciesTreeNodes
in interface GSDII
public SDIutil.TaxonomyComparisonBase getTaxCompBase()
getTaxCompBase
in interface GSDII
public final java.lang.String toString()
toString
in class java.lang.Object